1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
|
# Copyright 2000 Brad Chapman. All rights reserved.
# Revisions copyright 2007 Peter Cock. All rights reserved.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Example using Bio.SeqIO to load a FASTA file as a dictionary.
An example function (get_accession_num) is defined to demonstrate
a non-trivial naming scheme where the dictionary key is based on
the record identifier.
The first version uses Bio.SeqIO.parse() and loads the entire
FASTA file into memory as a Python dictionary of SeqRecord
objects. This is *not* suitable for large files.
The second version used Bio.SeqIO.index() which is suitable
for FASTA files with millions of records.
See also Bio.SeqIO.index_db() and the examples in the main tutorial.
"""
from Bio import SeqIO
def get_accession_num(seq_record):
"""Extract accession number from sequence id."""
accession_atoms = seq_record.id.split("|")
gb_name = accession_atoms[3]
# strip the version info before returning
return gb_name[:-2]
# In Memory
# =========
# This next bit of code uses Bio.SeqIO.parse() to load a FASTA file,
# and then turns it into an in-memory python dictionary.
# This is *not* suitable for FASTA files with millions of entries.
rec_iterator = SeqIO.parse("ls_orchid.fasta", "fasta")
orchid_dict = SeqIO.to_dict(rec_iterator, get_accession_num)
for id_num in orchid_dict:
print("id number: %s" % id_num)
print("description: %s" % orchid_dict[id_num].description)
print("sequence: %s" % orchid_dict[id_num].seq)
# Indexed
# =======
# This next version uses the Bio.SeqIO.index() function which will index
# the FASTA file without loading all the records into memory at once.
# This is suitable for FASTA files with millions of entries.
orchid_dict = SeqIO.index("ls_orchid.fasta", "fasta")
for id_num in orchid_dict:
print("id number: %s" % id_num)
print("description: %s" % orchid_dict[id_num].description)
print("sequence: %s" % orchid_dict[id_num].seq)
|
